MCP server

Wikipathways

io.github.pipeworx-io/wikipathways

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

WikiPathways MCP — open community pathway database.

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

45

Token cost

About 26,817 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http wikipathways https://gateway.pipeworx.io/wikipathways/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.wikipathways]
url = "https://gateway.pipeworx.io/wikipathways/mcp"

Gemini CLI

{"mcpServers":{"wikipathways":{"httpUrl":"https://gateway.pipeworx.io/wikipathways/mcp"}}}

Cursor

{"mcpServers":{"wikipathways":{"url":"https://gateway.pipeworx.io/wikipathways/mcp"}}}

VS Code

{"servers":{"wikipathways":{"type":"http","url":"https://gateway.pipeworx.io/wikipathways/mcp"}}}

Antigravity

agy mcp add wikipathways https://gateway.pipeworx.io/wikipathways/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"wikipathways","server_url":"https://gateway.pipeworx.io/wikipathways/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"wikipathways","server_url":"https://gateway.pipeworx.io/wikipathways/mcp"}

Tools

• get_pathway ~110 tokens
  Get metadata and a viewer link for one WikiPathways pathway by its WikiPathways id (e.g. "WP554"). Returns name, species, revision, and a human-viewable diagram URL. Keyless.
• list_pathways ~167 tokens
  List all WikiPathways pathways for a single organism. Give a Latin or common name, e.g. "Homo sapiens", "human", or "mouse". Returns each pathway's id, name, link, and last revision. Keyless.
• search_pathways ~237 tokens
  Search WikiPathways (open community pathway database) for biological pathways by name. Pathways map genes/proteins/metabolites in processes like glycolysis, apoptosis, or signaling. Optionally restrict to one organism by Latin or common name. Keyless. Complements KEGG/Reactome.

Browse

• GitHub tools
• GitHub and code hosting
• Databases

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